Choices
by criminalmindsforlife
Summary: What if it had been JJ with Reid in the compound  minimal loss  instead of Emily? Read to find out what happens when JJ makes a deal,a deal that changes everyones lives.Please R&R.
1. Chapter 1

**I hope you like it. Please R&R!**

"I want to know which one of you is the fbi agent!" The unsub, Cyrus, yelled at JJ and Reid, waving the gun in his hand around. JJ paled and noticed Reid had gotten really still as well. How did they know one of us was? JJ wondered. Looking over at Reid she could tell he wondered too. They had came undercover, using the position of social services workers to make sure the children who were living there weren't being treated bad. When Hotch told Reid and JJ to go they hadn't thought twice. Seeing Reid start to talk, to say it was him JJ took a step forward. "It's me. I'm the fbi agent." Reid looked at her sharply but JJ ignored him. Walking toward the man she held up her hands. "it's me." she repeated.

Cyrus nodded slowly and walked toward JJ slowly. He handed off the gun to a man beside him and reached for JJ. Grabbing a handful of her hair he pulled her close. " You think you can fucking lie to me! I'll fucking kill you and won't think twice." he yelled, his face just inches from hers. JJ didn't cry, wouldn't give him the satisfaction of crying. When he realized he wouldn't scare her enough that way dropped his grip from her hair, JJ fell on the floor at his feet.

He looked over at Reid and back to JJ. Pulling out his gun again he pointed it at JJ's head. She sat still, looking at Reid and holding his gaze. "Is she the fbi agent? Or was that a lie to?"

Reid didn't break his gaze from JJ and saw her giving him the look. Go along with whatever I say, she seemed to be telling him. Knowing it would be worse for her if he tried to say she wasn't the agent, he nodded. "She told me she was."

JJ sighed inwardly. Thank god Reid went along with it. He won't get hurt now. JJ thought, glad she could spare him this time. Last time he had been kidnapped, tortured and got addicted to drugs, all because she let him take the fall.

Cyrus looked down at JJ and smiled evilly. " Get up." he ordered. JJ stood up. Seeing Reid looked as if he was going to yell that he was the agent, and knowing the team needed some time before they could come in she looked at Cyrus and shook her head. "I'm up now what." She said smartly. Before she could blink she was laying on the ground, and Cyrus was kicking her. " Don't talk to me like that." JJ didn't cry out but tears were running down her cheeks. He finally stopped kicking her and pulled her up roughly by the arm. Nodding to the men standing beside Reid. "Take her upstairs till I can deal with her." JJ looked at Reid and smiled slightly, hoping to seem braver than she felt. "I'll be fine.' she mouthed as she was drug from the room.

JJ was tossed into a little room and left. She looked around, taking in every detail, hoping in some way it would help find a way out. No windows and only a small light. A bed, and chair. Other than that it was bare.

After what seemed like hours a woman walked into the room, carrying a bowl. She sat it down on the chair and looked at JJ, who was laying on the bed. She sat up, wincing at the sharp pain that shot through her sides. Definitely have broken ribs. The lady looked at her, lifting a clothe from the bowl of water she sat down beside JJ and leaned forward. Wiping the blood away from her face she started talking. "You shouldn't provoke him. You brought this on yourself."

JJ looked at the lady, and jerked backward. "Yeah I asked to be beat." she said sarcastically, wincing again from the pain.

Shaking her head the lady looked at JJ and squeezed her hand before standing back up. "You don't understand. He doesn't want to do this. God tells him to. You shouldn't argue with him."

JJ stood up and blocked the woman from leaving. " If you believe that, then why are you here helping me?"

"I was told to. Cyrus will be here to see you soon. If you agree with what he says and apologize you won't get hurt again." she pushed by JJ and started to leave. Stopping at the door she paused, not turning around. " Good luck."

JJ sat back down on the bed and thought about everything they knew, everything she remembered about the profile. Cyrus wouldn't just let them go. He was a control freak. He planned every little detail of everything. He had to have a plan for the way out, if something like this was to happen. They just had to figure out the plan and stop it.

The door opened again and Cyrus walked in. JJ didn't get up, just looked at him, wondering what he planned to do with her now, half afraid to find out.

He pulled the chair closer to the bed and sat down. Looking at JJ he watched her, not saying anything for a few minutes. JJ just stared back, which angered him. Deciding to see what would get a reaction from her he leaned forward. " I know your not the agent. But you took the fall for agent Reid."

JJ looked up sharply. "I'm the agent."

"Don't lie to me, Jennifer Jareau. I know your not the agent, just a media liaison. But I don't care now. I have a deal for you. A very generous deal, If I may add."

"I'm not making a deal with you." she stated, trying to stay calm. He couldn't hurt Reid.

"Oh, really?" he asked, smiling widely. "I'm pretty sure you will. You wouldn't want me to hurt agent Reid would you.?" he mockingly laughed.

JJ knew she had to take the deal. " What's the deal?" she asked quietly.

"I figured you would see it my way." he said snidely.

Getting up and shutting the door, he turned back to JJ. " The deal is, I won't kill agent Reid or you, but you have to do everything I tell you to, and not make a noise of complaint."

JJ instantly felt sick. Know telling what she would have to do. She started to shake her head, but thought of how Reid looked when they found him laying in the cemetery, almost dead. She paused, then holding her head up, not willing to let herself break down yet, she nodded. "You have a deal." Knowing the night was not going to end well JJ braced herself for what came next.

Cyrus looked surprised she took the deal. " Good. Now get up." Seeing JJ start to pause he held up his hand. " Remember, no complaining." JJ stood up, not feeling the pain in her sides, but a pain deep in the bottom of her stomach.. A mix between fear and dread.

**So whatcha think?**


	2. Chapter 2

As JJ heard Cyrus walk out of the room she finally let the tears fall. sobbing into the pillow she tried to picture good things, the team., her family, but nothing would come to mind. All she could see was Cyrus. She knew she had saved Reid's life, and her own, but JJ couldn't help but think of what it had cost her. The pain was horrible. She knew she would have bruises and need stitches. The team would see her, and never look at her the same. She tried to sit up, to try to find clothes to put on. She leaned over the side of the bed, spotting her shirt laying there. Grabbing it with one hand, she held her stomach with the other, not wanting to hurt her ribs more.

JJ had just pulled her shirt, and trying to reach her pants that were laying on the floor a few feet away when she heard shouting outside the door. She tried to move quickly, needing to get up and see what was going on. Struggling to stand she pulled her pants on, blocking out the pain by thinking she would be out of there soon.

She had just gotten her jeans on and was trying to get to the door when it was pushed open. "Fbi!" she heard Emily yell. "Oh my god, JJ!" was the last thing she heard before everything went black and she fell to the floor.

"Jennifer…. JJ I need you to wake up."

Looking up JJ saw a face a few inches from hers. Momentarily panicked she jerked back.

"JJ. Its ok. It's me.. It's Aaron." Hotch said, trying to calm her down. "JJ I need you to calm down. I'm going to lift you up, were going to take you to the hospital."

JJ started to struggle. "I need to find Reid, is he ok?" she demanded. Needing to know if Cyrus had kept their deal, or if she had been played.

"Reid's fine JJ. He's waiting for us outside."

JJ was starting to slip unconscious again. "Good. He kept our deal." she mumbled before everything went black.

"What deal is she talking about?" Hotch asked Emily confused. "Reid didn't say anything about a deal." Hotch held JJ and noticed the way her clothes were wrinkled and seemed to be torn. "Emily look around the room. Do you think he… do you think something happened to her?"

Emily glanced around and noticed the same thing Hotch did. " Hotch, we need to get her to the hospital. She needs to go now. We can talk to her when she gets checked out."

Hotch nodded and they left the room, Emily glancing back one last time, wondering what her friend had endured in that room.

"I told you I was ok to go home." JJ said stubbornly. "I don't need to stay overnight."

"JJ you have a concussion, 3 broke ribs, and stitches…you just woke up from being medicated. You are not going home yet." Hotch answered her, trying to be patient. He sat down on the edge of the bed. "JJ what happened in there."

JJ looked at her boss, trying to think of how to answer without having to tell him everything. He must have knew what she was doing though because before she could answer he started talking again. "JJ I know he abused you."

"Hotch, don't…just don't." JJ said evenly, hoping he would drop it.

"JJ. What deal were you talking about?" He asked her, watching her reaction. She looked at him, not showing emotion. "I had to.. He wouldn't hurt Spence… I did what he said.."

She broke off suddenly, emotion over taking her. She started crying and Hotch finally realized what she meant. "JJ. I'm so sorry." he said, pulling her carefully into a hug.

A few minutes later she had calmed down and sat back. "Don't tell anyone Hotch. Especially Reid. He can't know I was hurt to save him. It would hurt him worse, and he's been through enough with Hankel."

Hotch nodded slowly. "JJ I won't tell the team. This can stay between me and you. But you need to talk to someone, someone professional."

"No. I'm fine…well I will be fine." She almost yelled. "Why can't I just go home."

"I've told you. It's to late for you to leave today and-" he broke off when the door was flung open.

"JJ your awake!" Penelope exclaimed, rushing into the room. " Are you ok? I was so worried when we got the call! Poor Reid looks lost, he says you took the blame of being an agent for him!"

JJ looked at Hotch, letting him know she was right. Reid would blame himself enough for what he knew happened to her. Hotch nodded slightly, letting JJ know he would keep the secret.

"I'm fine Penelope. Just wanting to get out of here" she said honestly. She did want to get out of here, and she would be fine.

"Ok well I came to get the boss man and check up on you. The teams all waiting to hear how you are and Will is wanting to see you. I took the liberty of calling him myself, to let him know you was here so he can stay with you. we'll be back soon." Pulling Hotch with her she left. A few seconds later Will walked in, looking concerned, and kind of irritated.

"Hey." he said, walking toward the bed.

"Hey, sorry Penelope called you. I didn't know she was going to." JJ said, not wanting him to think she had started it.

"It's fine. I mean, I want to be here, I just…. It's hard JJ. I've asked you, plenty of times, to leave.. to move back to New Orleans with me. Your job is to dangerous, today proves it. You could have died." He said, getting madder with every word.

"Will. Stop." JJ said raising the bed up so she was sitting. "I am not giving up my job. I didn't tell you to give yours up and move here. We've had this conversation before and my answers not changing. I'm not leaving."

"JJ, know what?" Will said, backing toward the door, "I can't do this. I won't be second anymore. After a year you would think you would be more considerate of our life, instead of your job. Call me when you make that choice. Until then I'm done."

"Will…" JJ yelled as he stormed out the door.

The team was all standing in the waiting room, waiting to see JJ again before leaving. Watching as Will stormed out of her room they all wondered what was going on. Hotch thought JJ might have told him about the deal she had made. No one looked less surprised then Rossi. " They broke up a few days ago." he announced as the team continued to watch Will walk away.

Everyone turned to look at him. "What?" Penelope asked. She looked around upset. "I didn't know, I wouldn't have called if I did."

"How do you know they did?" Emily asked.

Rossi smiled grimly. "I was in my office about a week ago. I heard JJ answer her phone and then she started arguing. I wasn't trying to listen, but the walls are thin." he defended, seeing the team all look at him.

"Rights'." Derek said teasingly.

"Well she needs support now, so we'll be there for her." Penelope said determinately.

Hotch looked around at everyone. They was all rubbing there eyes, yawning and trying to stay awake. It'd been a long day. Glancing at his watch he saw it was almost 9. "Guys it's been a long day, go home. JJ's bound to be tired. I'll stay here tonight."

No one argued, but all said goodnight and left, promising to be back the next morning. Rossi stayed behind and looked at Aaron. "You go. You have Jack to look after. I'll stay and make sure she's ok."

"Rossi I don't know…"

"Hotch. It'll be fine. JJ will sleep and I'll make sure she's ok. Nothing's going to change between now and the morning." Rossi said, trying to reassure Hotch.

"Ok." he finally agreed. "But call if something does change."


	3. Chapter 3

Five weeks later JJ sat her desk reading a paper when there was a knock on her door. She shoved the paper in her desk and pulled a file down, acting like she was working on it. "Come in."

"Hey JJ you got plans for lunch?" Emily stood in the doorway. JJ had taken a week off and since she had came back the whole team had been treating her like glass. All inviting her to lunch, or supper, all kinds of stuff so she wouldn't be alone. They had been on one case since then, and she had done ok. Nightmares would find her some but other than that she was fine. While she appreciated her friends good gestures, it was getting kind of annoying.

"I think I'm going to work through lunch." JJ said, hoping Emily wouldn't think she was rude, she just needed to be alone. "Maybe tomorrow."

"Oh ok, well if you change your mind just be ready by 12." Emily said pulling her door shut as she left. JJ pulled the paper out and read the number at the top.

JJ lifted her office phone from its cradle and dialed the unfamiliar number from the paper. It rang five times and just as she figured It was going to go to voicemail it was answered. "Doctor Campbell's office, how may I help you?" a cheery voice said.

"Uhh yeah this is Jennifer Jareau. I need an appointment for lunchtime today, preferably with Doctor Peyton." She was one of JJ's old friends, and JJ hoped she could help her.

"We have one for 11:45. Is it possible for you to make that one?"

JJ looked at the clock. It was 11:15. If she left now she could make it. "Yeah that's fine. Thank you, I'll be there."

She hung up the phone and grabbed her pocketbook. Rushing out of the office she practically ran to the elevator. The team was all at there desks, and looked at her questionably when she ran past. She gave a quick wave. "Be back in an hour."

"Emily where's JJ going?" Hotch asked, walking from his office when he saw he run past.

"I don't know sir. She said she was going to work through lunch."

Derek walked up to Emily and Hotch, looking worried about JJ just leaving. "You want us to follow her?"

"No. JJ is a member of this team. We will not betray her trust. She deserves to have privacy."

Reid walked up to his co-workers who were gathered together. "What's going on, do we have a case?"

They all looked at him. "Reid, do you know where JJ went?" Hotch asked him.

"No…should I?" he asked, confused. "Is something wrong?"

"No. JJ had to take care of some things. She'll be back, like she said." Hotch said, basically letting the others no the conversation was over. "Get back to work."

He walked back to his office, trying to decide whether he was making the right decision by not finding out where JJ was going. She had been through a lot the past couple months, but she was doing better, or so he thought. He picked up his office phone and dialed her cell phone. It went to voicemail. Leaving a message telling her to call him he hung up the phone and sat down at his desk.

"JJ." The doctor greeted, walking into the exam room. " What can I do for you today?"

"I… I think I'm pregnant." JJ whispered. "I need to know for sure."

" Ok, well we can take some blood, and I can let you know by the end of the day. Why do you assume you are?" Her friend asked her, wondering why JJ didn't seem to thrilled about it.

"I've been sick lately, in the mornings, tired, and I missed my period." JJ answered her.

"Well we can take blood to double check but I would bet my next paycheck you are. Congratulations!" the doctor announced, but stopped short when she saw JJ's facial expression. "Is it not a good thing?"

JJ had gotten pale, and looked like she was going to pass out. " I was raped, this is the outcome."

"Oh my god! JJ what happened? Did you report it?"

"I was undercover for a case, the guy was shot and killed." JJ explained. " I told my boss, and its documented in the hospital report."

" I'm sorry. I know that doesn't help but I truly am. Are you doing ok?"

"Well this is a definite shock. I mean I didn't even think about this being a possibility. And when I got sick I just assumed it was the nightmares and lack of sleep. Then I missed my period and realized what it could be. Somehow I just knew, so I took a pregnancy test this morning, it was positive so I called and set up an appointment."

The doctor looked at JJ seriously. " Jennifer, you know there's always the option of-"

JJ held up her hand, shaking her head. "No! That's not an option for me. I couldn't do that. This baby-" JJ said pointing to her stomach, " didn't ask for this to happen to me. I couldn't do that. It may have been created badly, but it's still my baby."

"Calm down Jen. I had to give you the option." the doctor reached in a drawer and pulled out a paper. She scribbled something down and looked at JJ. " You said the attack was 6 weeks ago?" JJ nodded.

"Well if you have time I can do an ultrasound today. We can confirm it and you can see your baby."

JJ pulled out her phone and saw 4 missed calls. Two from Hotch, one from Emily and one from…Will? "Uhh well I might have to reschedule. My boss has called me a few times, we probably have a case…"

"Ok well call me later to set up an appointment. If possible in the next week. Here is a prescription for prenatal vitamins you need to take, and try to take it easy at work." she handed her a slip of paper, and a business card. "Call me if you need anything, no matter the time."

JJ thanked her again and left, wondering why Will would be calling her. They had talked one time since he left the hospital, the day she came home. She had told him again that she wasn't leaving, harsh words were exchanged and he packed up his stuff and left. Moving back to New Orleans.

She put her phone in her bag and tossed it all to the passenger seat, climbing into the car to head back to work.

**Hope you liked it.. please R&R!**

**Next chapter... any ideas on what should happen?**


	4. Chapter 4

JJ walked back into the office a half hour later. The entire team was sitting around Derek's desk. When JJ walked in and they all jumped up when they saw her. Hotch reached her first. "Where the hell have you been?" he demanded, his usual stoic mask was gone, replaced by worry and anger. JJ felt a twinge of guilt for not telling anyone anything, but it was gone as soon as he continued talking. "JJ if you need time off to deal with things then take it, but don't just leave without telling someone where your going."

She looked at Hotch who seemed to think she was a child. She thought about just walking away but the past couple months finally caught up with her. "Hotch, frankly its none of your business where I go during my lunch break."

The rest of the team were standing a few foot from them, eyeing JJ with surprise that she would talk to Hotch like that. Somehow that just made her madder. "I'm going to my office, if you have any other thoughts on how to run my life, shove em'." she moved past him and went into her office, slamming the door behind her.

Reid stared in shock. "JJ has never slammed a door.

Emily and Derek nodded, Garcia looked worried. "Hotch where has she been?"

Hotch shook his head, "She didn't say. I didn't mean for her to think I was trying to run her life, but she should have told someone where she was going."

Everyone agreed then split up, all going back to their work places, worrying about their blonde friend., hoping she was ok.

Rossi went back to his office and sat down at his desk. He was about to pick up a file and look over it when he heard JJ talking to someone. He sat back in his chair and listened, knowing it was wrong but not caring. They needed to know what was up with JJ and she obviously wasn't going to share with them anytime soon.

JJ was pacing her office and trying to vent her anger, without breaking something else. Her work phone started ringing and JJ snatched it up before the second ring. "Agent Jareau."

"Agent Jareau this is Pamela Greer. Chief Strauss has asked for me to call you and inform you that you have a meeting with her in an hour."

"Oh ok. Well thank you. Do you know what the meeting is in regards to?" JJ asked, hoping Hotch hadn't turned her in.

" No ma'am, I don't."

"Ok well thanks." JJ said, hanging up the phone.

Groaning JJ sat down at her desk, trying to think of a reason Erin Strauss would need to see her. Her eyes shifted to her door when she heard a light knock. "Come in."

Hotch walked in, looking uncertain, and apologetic. "JJ, I'm sorry about earlier."

JJ shook her head slowly, closing her eyes. "No you were right, I was out of line. You guys have all been supportive and I appreciate it. I overreacted."

"JJ why did you leave?" Hotch asked, taking a seat on the small couch.

"I had a doctors appointment. I didn't know about it till five minutes before I left, and didn't have time to explain everything then. I was going to when I got back but then you questioned me and I flipped."

"Doctors appointment?" Hotch asked, concern written on his face. "Are you ok?"

"I'm pregnant." JJ said.

Hotch was speechless. JJ was smiling so he took it as a good thing. "Congratulations right?"

JJ nodded slowly. "Yeah I'm happy, I just wish the circumstances were a lot different."

Hotch nodded, somberly remembering what JJ was referring to. "So it is" He searched for the right word. "his."

JJ shook her head. "Its not his. It's mine. He may be the sperm donor but that's it."

Hotch nodded thoughtfully. "JJ congratulations again. I'm sorry for me downing you in front of the team. Speaking of team, what are you going to tell them?"

JJ shrugged her shoulders. "Honestly I'm hoping they'll assume it's Wills."

"JJ you need to tell them. They'll understand. They won't-"

JJ stood up quickly. "No. If I tell them it's his then they'll ask what happened. Then It will come out about the deal, and I won't do that to Spencer."

Hotch knew that JJ felt guilty about Reid being hurt before. "JJ when are you going to realize that it's not your fault that Reid was hurt with Tobias. You didn't owe him for what happened. It was a mistake. People make them. Besides." he continued, "The team knows something happened. We are profilers. Eventually there going to realize it. Wouldn't you rather tell them now than them find out and have to explain later?"

"Hotch. I told you out of courtesy. You asked what was wrong and I told you. Not so you could grill me and try to make decisions for me. I'll tell them, just not right now. And as for them knowing something happened.. They don't know what right?" She was talking about the deal she had made.

Hotch shook his head. "Not a clue. I won't say anything until you do. So when are you going to tell them?"

"After I get the ultrasound done. So within the next week."

Hotch nodded and stood. "If you need anything, time off, anything, you let me know."

JJ nodded, then remembered her earlier phone call. "Did you call Strauss on me?"

"No." He answered, seeming as confused as she had been. "Why?"

"She wants to see me." glancing at her clock she realized she had to go. "I'm going to be late, so I have to go. I'll be back in an hour."

She walked quickly out of her office, Hotch followed, him going to his office and her to the elevator.

Rossi sat in his office. Slightly bewildered at what he had heard. JJ was pregnant, the outcome of the compound case. He had known something had happened in there that had changed her but wasn't exactly sure what until know. She had made some deal ,and because of that deal, she didn't want the team to know that she was pregnant yet. Rossi stood up, trying to process everything. It was a lot for him, he wondered how JJ was doing it. He thought about confronting her, but knew she would be upset if she knew he had listened to a private conversation. Especially one that was that important. Sitting back down he wondered if he could use this news to his advantage. He had been trying to think of a way to tell JJ how he felt about her since he had stayed that night with her in the hospital. It always seemed like the wrong time, and now he learned she was pregnant. Not that that was a bad thing, if she was happy he was. But now knowing what he did, he realized it didn't change anything. He still cared for her, even more so now, hearing how she had handled everything. She could be yelling, blaming so one else, or trying to get rid of the baby. Instead she loved it already, smiling as he remembering her voice when she had corrected Aaron's response about the father. Knowing he would have to tell her soon.

**Sooo? Please Read and Review. Thanks for reading! Sorry it took so long. School exams were this week and I've been busy with them, and trying to think of what happens next in the story. Any ideas? Let me know!:D Oh and in this story Haley was never killed and her and Hotch are still married.**


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